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- EMDB-53795: 5-Helix Tile - Twist Corrected (5HT-TC) with 2'-Fluoro-modified p... -

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Basic information

Entry
Database: EMDB / ID: EMD-53795
Title5-Helix Tile - Twist Corrected (5HT-TC) with 2'-Fluoro-modified pyrimidines (FY RNA)
Map datacryo-EM map of 2-prime-fluoro-modified pyrimidine RNA 5-Helix Tile - Twist Corrected (5HT-TC) origami structure.
Sample
  • Complex: Single-stranded 5HT-monomer made of 2'fluoro modified pyrimidine RNA
    • RNA: DNA/RNA (552-MER)
Keywordsorigami / modified nucleic acids / XNA / RNA / crossover / tetra-loop / kissing-loop / 2'fluoro
Biological speciessynthetic construct (others) / synthetic RNA (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.06 Å
AuthorsKristoffersen EL / Andersen ES / Zwergius NH
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF21OC0070452 Denmark
CitationJournal: To Be Published
Title: Serum-stable RNA origami nanodevices
Authors: Kristoffersen EL / Zwergius NH / Vallina NS / Gluck N / Stange A / Desdorf L / Civit L / Geary C / Kjems J / Valero J / Andersen ES
History
DepositionMay 15, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53795.png

Downloads & links

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Map

FileDownload / File: emd_53795.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map of 2-prime-fluoro-modified pyrimidine RNA 5-Helix Tile - Twist Corrected (5HT-TC) origami structure.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 256 pix.
= 331.264 Å		1.29 Å/pix.
x 256 pix.
= 331.264 Å		1.29 Å/pix.
x 256 pix.
= 331.264 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.294 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.13129012 - 0.49716243
Average (Standard dev.)0.00013141197 (±0.019113163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 331.264 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A of 2-prime-fluoro-modified pyrimidine RNA 5-Helix...

Fileemd_53795_half_map_1.map
AnnotationHalf map A of 2-prime-fluoro-modified pyrimidine RNA 5-Helix Tile - Twist Corrected (5HT-TC) origami structure
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of 2-prime-fluoro-modified pyrimidine RNA 5-Helix...

Fileemd_53795_half_map_2.map
AnnotationHalf map B of 2-prime-fluoro-modified pyrimidine RNA 5-Helix Tile - Twist Corrected (5HT-TC) origami structure
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Single-stranded 5HT-monomer made of 2'fluoro modified pyrimidine RNA

EntireName: Single-stranded 5HT-monomer made of 2'fluoro modified pyrimidine RNA
Components
  • Complex: Single-stranded 5HT-monomer made of 2'fluoro modified pyrimidine RNA
    • RNA: DNA/RNA (552-MER)

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Supramolecule #1: Single-stranded 5HT-monomer made of 2'fluoro modified pyrimidine RNA

SupramoleculeName: Single-stranded 5HT-monomer made of 2'fluoro modified pyrimidine RNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: In vitro transcribed using mutant (Y639F) T7 RNA polymerase
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: DNA/RNA (552-MER)

MacromoleculeName: DNA/RNA (552-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic RNA (others)
Molecular weightTheoretical: 178.265078 KDa
SequenceString: GGG(CFZ)A(CFZ)(UFT)(UFT)A(CFZ) (CFZ)(CFZ)(UFT)(UFT)(UFT)AG(UFT)G(CFZ) GAAGG(UFT) (UFT)(UFT)(CFZ) GA(CFZ)(CFZ)(UFT)(UFT)(CFZ)GA(UFT) (CFZ)(CFZ)A(UFT)(UFT)(UFT)G (UFT)(UFT) (CFZ)G(CFZ)AAA(UFT) ...String:
GGG(CFZ)A(CFZ)(UFT)(UFT)A(CFZ) (CFZ)(CFZ)(UFT)(UFT)(UFT)AG(UFT)G(CFZ) GAAGG(UFT) (UFT)(UFT)(CFZ) GA(CFZ)(CFZ)(UFT)(UFT)(CFZ)GA(UFT) (CFZ)(CFZ)A(UFT)(UFT)(UFT)G (UFT)(UFT) (CFZ)G(CFZ)AAA(UFT)GGG A(UFT)GA(UFT)(CFZ)(UFT)(UFT)(CFZ)G GA(UFT)(CFZ)A (UFT)(CFZ)(CFZ)G (CFZ)G(UFT)AG(UFT)(CFZ)(UFT)G(UFT) (UFT)(CFZ)AG(UFT)(CFZ)G(UFT) (UFT) (UFT)(CFZ)GA(CFZ)GA(CFZ)(UFT)G G(CFZ)(CFZ)(CFZ)(CFZ)A(CFZ)(UFT)(UFT)(CFZ) GG (UFT)GGGG(CFZ)(CFZ) A(CFZ)GG(UFT)A(CFZ)(UFT)(UFT)A GAAG(UFT)GAA(CFZ)A (CFZ)(UFT)AAG (UFT)G(UFT)(CFZ) G(UFT)GAA(CFZ)A(CFZ)(CFZ)A (UFT)(UFT)(UFT)GG(UFT)(UFT)AA(CFZ) (UFT)G(CFZ)(UFT)(CFZ)AAA(CFZ) (UFT)AAA(UFT)GG(UFT)GA (UFT)GAGGGAAGG AA(UFT)GA(CFZ) (CFZ)(CFZ)(UFT) (CFZ)A(UFT)(CFZ)GGA(CFZ)(UFT)A (CFZ)G(CFZ)GA(UFT)(CFZ)(CFZ)GA G (UFT)GA(UFT)GGGA A(UFT)GG(CFZ)(UFT)GA(CFZ)(CFZ) (CFZ)A(UFT)(CFZ)G(CFZ)(UFT)(CFZ)GG (CFZ)A(CFZ)(UFT)GGAGG G(UFT)GAG(UFT)G(CFZ)(CFZ)(CFZ) (CFZ)(UFT)(CFZ)A(UFT)(UFT) (CFZ)G(CFZ) A(UFT)AAGGG(CFZ)(CFZ)G A(CFZ)(CFZ)(CFZ)AGA(CFZ)AA (CFZ)AG(CFZ)(CFZ)AAG (UFT) (UFT)(UFT)GGG(UFT)(CFZ)GGA GA(UFT)G(CFZ)GAA(CFZ)A (UFT)(UFT)(CFZ)(CFZ)A(CFZ)G (CFZ)A (UFT)(CFZ)(UFT)GAA(CFZ)GG(UFT) (UFT)GAGAA(CFZ)(UFT)(UFT)A (CFZ)AAGGG(CFZ)AAG AG(CFZ)AGAG(UFT)(CFZ) (CFZ)(UFT)(UFT)G(UFT)AAGGG (CFZ)(UFT)(UFT)(UFT)A(CFZ)A(CFZ)G (UFT)(CFZ)AAG(UFT)(UFT)(CFZ)A(CFZ) AGA(CFZ)G(UFT)G(UFT)AA GG(CFZ)(CFZ)(CFZ)G(UFT) (CFZ)G (CFZ)(CFZ)(CFZ)(UFT)(UFT)(CFZ)GGGG (CFZ)GA(CFZ)G(UFT)(UFT)(CFZ)A(CFZ) GG (CFZ)A(UFT)(UFT)(UFT)(CFZ)G A(UFT)G(CFZ)(CFZ)G(UFT)G(CFZ)A G(CFZ)(CFZ)(UFT)G(UFT) (UFT)(CFZ)G (CFZ)AGG(CFZ)(UFT)G(CFZ)(UFT)(UFT) GA(CFZ)(CFZ)G(UFT)(UFT)(CFZ)(CFZ) (CFZ)(CFZ)(UFT)G(CFZ)(CFZ)(CFZ)(UFT)(UFT)(UFT) (CFZ)GAGGG(CFZ)AGA (CFZ)(UFT)A(CFZ) (UFT)(CFZ)(UFT)(UFT)(CFZ) GGAG(UFT)AG(UFT)(CFZ)(UFT) (UFT)A(UFT)G(UFT)GAA(UFT)G AG

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationNameFormula
40.0 mMHEPES
5.0 mMMagnesium ChlorideMgCl2
50.0 mMPotassium ChlorideKCl
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4449 / Average exposure time: 1.5 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 314600
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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